Overview

Perform DESeq2 and related analysis on 6 different datasets: * miRNA counts generated by sRNAde * miRNA counts parsed from sRNAbench (the same data as above, but with more miRNAs) * ncRNA counts parsed from sRNAbench * tRNA counts parsed from sRNAbench * cDNA counts parsed from sRNAbench * a dataset contains all types of small RNAs using another dataset

For each of the dataset, perform the following preprocessing procedure: 1. remove Library_24 and Library_33, as by QC they have problems like low counts 2. filter out small RNAs with less than 10 counts across all libraries

miRNA from sRNAde

We first analyze the miRNA read counts generated by sRNAde.

sample-wise heatmap

  • rows and columns clustered
  • label = library+dosages

PCA plots

  • From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder.
  • The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18) /folder.
  • It is interesting that the datapoints labeled with dosage roughly form a spectrum on PC1.

DESeq with Wald test

  • dosage 50mg vs 0mg results (only print the top 10 miRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## Wald test p-value: dosage 50 vs 0 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-200b-3p  48.78561       1.653585  0.349556   4.73053 2.23931e-06
## rno-miR-221-3p   29.41731       2.122209  0.493184   4.30308 1.68439e-05
## rno-let-7c-5p   163.30752       1.419720  0.409246   3.46911 5.22186e-04
## rno-miR-429      19.94727       1.403375  0.412940   3.39850 6.77570e-04
## rno-miR-365-3p    7.72493       1.821033  0.553912   3.28759 1.01049e-03
## rno-miR-205      31.13048       1.544480  0.491664   3.14133 1.68181e-03
## rno-miR-23a-3p  108.38653       0.975798  0.327285   2.98150 2.86843e-03
## rno-miR-24-3p    58.19679       1.244753  0.422272   2.94775 3.20092e-03
## rno-let-7b-5p    79.33072       1.089664  0.384765   2.83203 4.62538e-03
## rno-miR-871-3p    8.09010       1.445964  0.535561   2.69990 6.93593e-03
##                        padj
##                   <numeric>
## rno-miR-200b-3p 0.000179145
## rno-miR-221-3p  0.000673754
## rno-let-7c-5p   0.013551409
## rno-miR-429     0.013551409
## rno-miR-365-3p  0.016167902
## rno-miR-205     0.022424138
## rno-miR-23a-3p  0.032009227
## rno-miR-24-3p   0.032009227
## rno-let-7b-5p   0.041114465
## rno-miR-871-3p  0.055487445
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## Wald test p-value: dosage 60 vs 0 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-221-3p    29.4173        3.54509  0.500999   7.07605 1.48319e-12
## rno-miR-200b-3p   48.7856        2.20786  0.359500   6.14149 8.17489e-10
## rno-miR-429       19.9473        2.46121  0.419608   5.86550 4.47774e-09
## rno-miR-205       31.1305        2.92857  0.500489   5.85142 4.87391e-09
## rno-miR-10a-5p   114.3573        2.08064  0.357632   5.81783 5.96174e-09
## rno-miR-24-3p     58.1968        2.34332  0.432226   5.42152 5.90941e-08
## rno-miR-145-5p   289.3245        1.90685  0.354328   5.38161 7.38218e-08
## rno-miR-23a-3p   108.3865        1.72876  0.335978   5.14545 2.66874e-07
## rno-miR-22-3p     54.7086        2.40169  0.480464   4.99869 5.77211e-07
## rno-miR-320-3p    14.7781        2.78132  0.574202   4.84380 1.27376e-06
##                        padj
##                   <numeric>
## rno-miR-221-3p  1.18655e-10
## rno-miR-200b-3p 3.26996e-08
## rno-miR-429     9.53879e-08
## rno-miR-205     9.53879e-08
## rno-miR-10a-5p  9.53879e-08
## rno-miR-24-3p   7.87921e-07
## rno-miR-145-5p  8.43678e-07
## rno-miR-23a-3p  2.66874e-06
## rno-miR-22-3p   5.13077e-06
## rno-miR-320-3p  1.01901e-05
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## Wald test p-value: dosage 75 vs 0 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-200b-3p   48.7856        2.88793  0.363240   7.95049 1.85769e-15
## rno-miR-429       19.9473        3.27752  0.425455   7.70356 1.32323e-14
## rno-miR-221-3p    29.4173        3.78480  0.508133   7.44843 9.44541e-14
## rno-miR-10a-5p   114.3573        2.59696  0.359572   7.22237 5.10891e-13
## rno-miR-205       31.1305        3.20308  0.507005   6.31765 2.65576e-10
## rno-miR-23a-3p   108.3865        1.76838  0.340275   5.19692 2.02616e-07
## rno-miR-29a-3p    87.5367        1.79645  0.361240   4.97299 6.59268e-07
## rno-miR-22-3p     54.7086        2.41307  0.485496   4.97031 6.68446e-07
## rno-miR-10b-5p    91.1628        1.44507  0.292337   4.94315 7.68687e-07
## rno-miR-871-3p     8.0901        2.65986  0.565270   4.70546 2.53291e-06
##                        padj
##                   <numeric>
## rno-miR-200b-3p 1.48615e-13
## rno-miR-429     5.29293e-13
## rno-miR-221-3p  2.51878e-12
## rno-miR-10a-5p  1.02178e-11
## rno-miR-205     4.24922e-09
## rno-miR-23a-3p  2.70154e-06
## rno-miR-29a-3p  6.68446e-06
## rno-miR-22-3p   6.68446e-06
## rno-miR-10b-5p  6.83278e-06
## rno-miR-871-3p  1.91822e-05

Volcano plots for DESeq with Wald test

DESeq with likelihood ratio test

Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.

  • dosage 50mg vs 0mg results (only print the top 10 miRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-429       19.9473       1.403375  0.412940   64.1291 7.70233e-14
## rno-miR-200b-3p   48.7856       1.653585  0.349556   60.4358 4.74383e-13
## rno-miR-10a-5p   114.3573       0.918542  0.349446   59.0682 9.29613e-13
## rno-miR-221-3p    29.4173       2.122209  0.493184   58.1286 1.47558e-12
## rno-miR-205       31.1305       1.544480  0.491664   44.3393 1.27839e-09
## rno-miR-22-3p     54.7086       0.297279  0.473674   42.1150 3.79283e-09
## rno-miR-145-5p   289.3245       0.682316  0.345690   34.6466 1.44673e-07
## rno-miR-23a-3p   108.3865       0.975798  0.327285   32.4929 4.11984e-07
## rno-miR-10b-5p    91.1628       0.301981  0.280696   31.5731 6.43782e-07
## rno-miR-24-3p     58.1968       1.244753  0.422272   30.3081 1.18870e-06
##                        padj
##                   <numeric>
## rno-miR-429     6.16186e-12
## rno-miR-200b-3p 1.89753e-11
## rno-miR-10a-5p  2.47897e-11
## rno-miR-221-3p  2.95117e-11
## rno-miR-205     2.04543e-08
## rno-miR-22-3p   5.05711e-08
## rno-miR-145-5p  1.65340e-06
## rno-miR-23a-3p  4.11984e-06
## rno-miR-10b-5p  5.72250e-06
## rno-miR-24-3p   9.50960e-06
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-429       19.9473        2.46121  0.419608   64.1291 7.70233e-14
## rno-miR-200b-3p   48.7856        2.20786  0.359500   60.4358 4.74383e-13
## rno-miR-10a-5p   114.3573        2.08064  0.357632   59.0682 9.29613e-13
## rno-miR-221-3p    29.4173        3.54509  0.500999   58.1286 1.47558e-12
## rno-miR-205       31.1305        2.92857  0.500489   44.3393 1.27839e-09
## rno-miR-22-3p     54.7086        2.40169  0.480464   42.1150 3.79283e-09
## rno-miR-145-5p   289.3245        1.90685  0.354328   34.6466 1.44673e-07
## rno-miR-23a-3p   108.3865        1.72876  0.335978   32.4929 4.11984e-07
## rno-miR-10b-5p    91.1628        1.05431  0.288295   31.5731 6.43782e-07
## rno-miR-24-3p     58.1968        2.34332  0.432226   30.3081 1.18870e-06
##                        padj
##                   <numeric>
## rno-miR-429     6.16186e-12
## rno-miR-200b-3p 1.89753e-11
## rno-miR-10a-5p  2.47897e-11
## rno-miR-221-3p  2.95117e-11
## rno-miR-205     2.04543e-08
## rno-miR-22-3p   5.05711e-08
## rno-miR-145-5p  1.65340e-06
## rno-miR-23a-3p  4.11984e-06
## rno-miR-10b-5p  5.72250e-06
## rno-miR-24-3p   9.50960e-06
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-429       19.9473        3.27752  0.425455   64.1291 7.70233e-14
## rno-miR-200b-3p   48.7856        2.88793  0.363240   60.4358 4.74383e-13
## rno-miR-10a-5p   114.3573        2.59696  0.359572   59.0682 9.29613e-13
## rno-miR-221-3p    29.4173        3.78480  0.508133   58.1286 1.47558e-12
## rno-miR-205       31.1305        3.20308  0.507005   44.3393 1.27839e-09
## rno-miR-22-3p     54.7086        2.41307  0.485496   42.1150 3.79283e-09
## rno-miR-145-5p   289.3245        1.63288  0.356304   34.6466 1.44673e-07
## rno-miR-23a-3p   108.3865        1.76838  0.340275   32.4929 4.11984e-07
## rno-miR-10b-5p    91.1628        1.44507  0.292337   31.5731 6.43782e-07
## rno-miR-24-3p     58.1968        2.00698  0.440226   30.3081 1.18870e-06
##                        padj
##                   <numeric>
## rno-miR-429     6.16186e-12
## rno-miR-200b-3p 1.89753e-11
## rno-miR-10a-5p  2.47897e-11
## rno-miR-221-3p  2.95117e-11
## rno-miR-205     2.04543e-08
## rno-miR-22-3p   5.05711e-08
## rno-miR-145-5p  1.65340e-06
## rno-miR-23a-3p  4.11984e-06
## rno-miR-10b-5p  5.72250e-06
## rno-miR-24-3p   9.50960e-06

Volcano plots for DESeq with likelihood ratio test

heatmap of counts

  • columns clustered
  • show miRNAs of top 20 mean counts



miRNA counts parsed from sRNAbench results

Repeat the above analysis on miRNA counts parsed from sRNAbench results

sample-wise heatmap

  • rows and columns clustered
  • label = library+dosages

PCA plots

  • From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder.
  • The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18) /folder.
  • Compared to the 80-miRNA results from sRNAde, the plots look much different.
  • The spectrum-like distribution of data over dosage PC1 also appears here.

DESeq with Wald test

Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”

  • dosage 50mg vs 0mg results (only print the top 10 miRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## Wald test p-value: dosage 50 vs 0 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-200b-3p  48.78561       1.653561  0.349300   4.73393 2.20214e-06
## rno-miR-221-3p   29.41731       2.123987  0.501352   4.23652 2.27013e-05
## rno-miR-200a-3p  12.16107       2.710952  0.739204   3.66739 2.45037e-04
## rno-let-7c-5p   163.30752       1.419870  0.411958   3.44664 5.67611e-04
## rno-miR-429      19.94727       1.402210  0.415639   3.37362 7.41858e-04
## rno-miR-365-3p    7.72493       1.824171  0.568647   3.20792 1.33701e-03
## rno-miR-27a-3p    9.23401       2.119159  0.674050   3.14392 1.66702e-03
## rno-miR-205      31.13048       1.544651  0.501779   3.07835 2.08153e-03
## rno-miR-23a-3p  108.38653       0.975648  0.325839   2.99427 2.75103e-03
## rno-miR-24-3p    58.19679       1.245022  0.426453   2.91948 3.50612e-03
##                        padj
##                   <numeric>
## rno-miR-200b-3p 0.000266459
## rno-miR-221-3p  0.001373429
## rno-miR-200a-3p 0.009883165
## rno-let-7c-5p   0.017170222
## rno-miR-429     0.017952965
## rno-miR-365-3p  0.026962981
## rno-miR-27a-3p  0.028815634
## rno-miR-205     0.031483182
## rno-miR-23a-3p  0.036986119
## rno-miR-24-3p   0.042424080
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## Wald test p-value: dosage 60 vs 0 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-221-3p    29.4173        3.54476  0.509464   6.95782 3.45589e-12
## rno-miR-200b-3p   48.7856        2.20791  0.359236   6.14613 7.93944e-10
## rno-miR-429       19.9473        2.46179  0.422390   5.82823 5.60192e-09
## rno-miR-10a-5p   114.3573        2.08066  0.357199   5.82492 5.71396e-09
## rno-miR-205       31.1305        2.92917  0.510933   5.73299 9.86747e-09
## rno-miR-145-5p   289.3245        1.90689  0.353461   5.39490 6.85621e-08
## rno-miR-148a-3p    7.3813        4.67085  0.868366   5.37889 7.49451e-08
## rno-miR-24-3p     58.1968        2.34345  0.436527   5.36839 7.94427e-08
## rno-miR-23a-3p   108.3865        1.72886  0.334493   5.16860 2.35849e-07
## rno-miR-22-3p     54.7086        2.40148  0.488855   4.91245 8.99431e-07
##                        padj
##                   <numeric>
## rno-miR-221-3p  6.56620e-10
## rno-miR-200b-3p 7.54247e-08
## rno-miR-429     2.71413e-07
## rno-miR-10a-5p  2.71413e-07
## rno-miR-205     3.74964e-07
## rno-miR-145-5p  1.88676e-06
## rno-miR-148a-3p 1.88676e-06
## rno-miR-24-3p   1.88676e-06
## rno-miR-23a-3p  4.97904e-06
## rno-miR-22-3p   1.70892e-05
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## Wald test p-value: dosage 75 vs 0 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-200b-3p   48.7856        2.88796  0.362979   7.95627 1.77303e-15
## rno-miR-429       19.9473        3.27700  0.428205   7.65289 1.96510e-14
## rno-miR-221-3p    29.4173        3.78447  0.516494   7.32723 2.34953e-13
## rno-miR-10a-5p   114.3573        2.59699  0.359141   7.23111 4.79054e-13
## rno-miR-205       31.1305        3.20284  0.517336   6.19102 5.97753e-10
## rno-miR-148a-3p    7.3813        5.09314  0.879899   5.78833 7.10908e-09
## rno-miR-200a-3p   12.1611        4.31140  0.760779   5.66709 1.45246e-08
## rno-miR-451-5p    21.7035        4.06731  0.746619   5.44764 5.10422e-08
## rno-miR-23a-3p   108.3865        1.76816  0.338809   5.21875 1.80138e-07
## rno-miR-10b-5p    91.1628        1.44573  0.287609   5.02671 4.98955e-07
##                        padj
##                   <numeric>
## rno-miR-200b-3p 3.65244e-13
## rno-miR-429     2.02405e-12
## rno-miR-221-3p  1.61335e-11
## rno-miR-10a-5p  2.46713e-11
## rno-miR-205     2.46274e-08
## rno-miR-148a-3p 2.44078e-07
## rno-miR-200a-3p 4.27437e-07
## rno-miR-451-5p  1.31434e-06
## rno-miR-23a-3p  4.12315e-06
## rno-miR-10b-5p  1.02785e-05

Volcano plots for DESeq with Wald test

DESeq with likelihood ratio test

Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.

  • dosage 50mg vs 0mg results (only print the top 10 miRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-429       19.9473       1.402210  0.415639   63.2288 1.19992e-13
## rno-miR-200b-3p   48.7856       1.653561  0.349300   60.5285 4.53248e-13
## rno-miR-10a-5p   114.3573       0.918552  0.349026   59.2134 8.65507e-13
## rno-miR-221-3p    29.4173       2.123987  0.501352   56.0467 4.10555e-12
## rno-miR-205       31.1305       1.544651  0.501779   42.4798 3.17350e-09
## rno-miR-22-3p     54.7086       0.296728  0.481784   40.6700 7.68260e-09
## rno-miR-148a-3p    7.3813       2.518737  0.872444   40.5696 8.06874e-09
## rno-miR-145-5p   289.3245       0.682294  0.344846   34.8190 1.33037e-07
## rno-miR-23a-3p   108.3865       0.975648  0.325839   32.7820 3.58043e-07
## rno-miR-10b-5p    91.1628       0.301678  0.276035   32.6708 3.77894e-07
##                        padj
##                   <numeric>
## rno-miR-429     2.08787e-11
## rno-miR-200b-3p 3.94326e-11
## rno-miR-10a-5p  5.01994e-11
## rno-miR-221-3p  1.78591e-10
## rno-miR-205     1.10438e-07
## rno-miR-22-3p   2.00566e-07
## rno-miR-148a-3p 2.00566e-07
## rno-miR-145-5p  2.89355e-06
## rno-miR-23a-3p  6.57536e-06
## rno-miR-10b-5p  6.57536e-06
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-429       19.9473        2.46179  0.422390   63.2288 1.19992e-13
## rno-miR-200b-3p   48.7856        2.20791  0.359236   60.5285 4.53248e-13
## rno-miR-10a-5p   114.3573        2.08066  0.357199   59.2134 8.65507e-13
## rno-miR-221-3p    29.4173        3.54476  0.509464   56.0467 4.10555e-12
## rno-miR-205       31.1305        2.92917  0.510933   42.4798 3.17350e-09
## rno-miR-22-3p     54.7086        2.40148  0.488855   40.6700 7.68260e-09
## rno-miR-148a-3p    7.3813        4.67085  0.868366   40.5696 8.06874e-09
## rno-miR-145-5p   289.3245        1.90689  0.353461   34.8190 1.33037e-07
## rno-miR-23a-3p   108.3865        1.72886  0.334493   32.7820 3.58043e-07
## rno-miR-10b-5p    91.1628        1.05489  0.283505   32.6708 3.77894e-07
##                        padj
##                   <numeric>
## rno-miR-429     2.08787e-11
## rno-miR-200b-3p 3.94326e-11
## rno-miR-10a-5p  5.01994e-11
## rno-miR-221-3p  1.78591e-10
## rno-miR-205     1.10438e-07
## rno-miR-22-3p   2.00566e-07
## rno-miR-148a-3p 2.00566e-07
## rno-miR-145-5p  2.89355e-06
## rno-miR-23a-3p  6.57536e-06
## rno-miR-10b-5p  6.57536e-06
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                  baseMean log2FoldChange     lfcSE      stat      pvalue
##                 <numeric>      <numeric> <numeric> <numeric>   <numeric>
## rno-miR-429       19.9473        3.27700  0.428205   63.2288 1.19992e-13
## rno-miR-200b-3p   48.7856        2.88796  0.362979   60.5285 4.53248e-13
## rno-miR-10a-5p   114.3573        2.59699  0.359141   59.2134 8.65507e-13
## rno-miR-221-3p    29.4173        3.78447  0.516494   56.0467 4.10555e-12
## rno-miR-205       31.1305        3.20284  0.517336   42.4798 3.17350e-09
## rno-miR-22-3p     54.7086        2.41256  0.493812   40.6700 7.68260e-09
## rno-miR-148a-3p    7.3813        5.09314  0.879899   40.5696 8.06874e-09
## rno-miR-145-5p   289.3245        1.63294  0.355442   34.8190 1.33037e-07
## rno-miR-23a-3p   108.3865        1.76816  0.338809   32.7820 3.58043e-07
## rno-miR-10b-5p    91.1628        1.44573  0.287609   32.6708 3.77894e-07
##                        padj
##                   <numeric>
## rno-miR-429     2.08787e-11
## rno-miR-200b-3p 3.94326e-11
## rno-miR-10a-5p  5.01994e-11
## rno-miR-221-3p  1.78591e-10
## rno-miR-205     1.10438e-07
## rno-miR-22-3p   2.00566e-07
## rno-miR-148a-3p 2.00566e-07
## rno-miR-145-5p  2.89355e-06
## rno-miR-23a-3p  6.57536e-06
## rno-miR-10b-5p  6.57536e-06

Volcano plots for DESeq with likelihood ratio test

heatmap of counts

  • columns clustered
  • show miRNAs of top 20 mean counts



tRNA counts parsed from sRNAbench results

Repeat the above analysis on tRNA counts parsed from sRNAbench results

sample-wise heatmap

  • rows and columns clustered
  • label = library+dosages

PCA plots

  • From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder
  • The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18).
  • The spectrum-like distribution of data over dosage PC1 still observable.
  • Library_06 as an outlier?

DESeq with Wald test

Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”

  • dosage 50mg vs 0mg results (only print the top 10 tRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## Wald test p-value: dosage 50 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                    baseMean log2FoldChange
##                                                   <numeric>      <numeric>
## Rattus_norvegicus_chr1.trna16347-GluCTC:tRNA      6433.5762       1.142110
## Rattus_norvegicus_chr10.trna11370-GluCTC:tRNA     6433.5762       1.142110
## Rattus_norvegicus_chr13.trna2187-GluCTC:tRNA      6433.5762       1.142110
## Rattus_norvegicus_chr13.trna3809-GluCTC:tRNA      6433.5762       1.142110
## Rattus_norvegicus_chr13_random.trna22-GluCTC:tRNA 6433.5762       1.142110
## Rattus_norvegicus_chr13_random.trna25-GluCTC:tRNA 6433.5762       1.142110
## Rattus_norvegicus_chr17.trna1684-GluCTC:tRNA      6433.5762       1.142110
## Rattus_norvegicus_chr2.trna7260-GluCTC:tRNA       6433.5762       1.142110
## Rattus_norvegicus_chr2.trna7274-GlyCCC:tRNA        377.2421       0.473923
## Rattus_norvegicus_chr16.trna1087-GluTTC:tRNA        21.3227       1.444513
##                                                       lfcSE      stat
##                                                   <numeric> <numeric>
## Rattus_norvegicus_chr1.trna16347-GluCTC:tRNA       0.331765   3.44253
## Rattus_norvegicus_chr10.trna11370-GluCTC:tRNA      0.331765   3.44253
## Rattus_norvegicus_chr13.trna2187-GluCTC:tRNA       0.331765   3.44253
## Rattus_norvegicus_chr13.trna3809-GluCTC:tRNA       0.331765   3.44253
## Rattus_norvegicus_chr13_random.trna22-GluCTC:tRNA  0.331765   3.44253
## Rattus_norvegicus_chr13_random.trna25-GluCTC:tRNA  0.331765   3.44253
## Rattus_norvegicus_chr17.trna1684-GluCTC:tRNA       0.331765   3.44253
## Rattus_norvegicus_chr2.trna7260-GluCTC:tRNA        0.331765   3.44253
## Rattus_norvegicus_chr2.trna7274-GlyCCC:tRNA        0.143668   3.29874
## Rattus_norvegicus_chr16.trna1087-GluTTC:tRNA       0.500256   2.88755
##                                                        pvalue      padj
##                                                     <numeric> <numeric>
## Rattus_norvegicus_chr1.trna16347-GluCTC:tRNA      0.000576306 0.0262940
## Rattus_norvegicus_chr10.trna11370-GluCTC:tRNA     0.000576306 0.0262940
## Rattus_norvegicus_chr13.trna2187-GluCTC:tRNA      0.000576306 0.0262940
## Rattus_norvegicus_chr13.trna3809-GluCTC:tRNA      0.000576306 0.0262940
## Rattus_norvegicus_chr13_random.trna22-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr13_random.trna25-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr17.trna1684-GluCTC:tRNA      0.000576306 0.0262940
## Rattus_norvegicus_chr2.trna7260-GluCTC:tRNA       0.000576306 0.0262940
## Rattus_norvegicus_chr2.trna7274-GlyCCC:tRNA       0.000971205 0.0393878
## Rattus_norvegicus_chr16.trna1087-GluTTC:tRNA      0.003882543 0.1417128
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## Wald test p-value: dosage 60 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                baseMean log2FoldChange
##                                               <numeric>      <numeric>
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA   162.4158        1.78386
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA  162.4158        1.78386
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA   162.4158        1.78386
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA    222.4611        1.27260
## Rattus_norvegicus_chrUn.trna406-LysCTT:tRNA     21.1984        1.52026
## Rattus_norvegicus_chr10.trna12028-LysCTT:tRNA 3847.5061        1.38571
## Rattus_norvegicus_chr10.trna12844-LysCTT:tRNA 3847.5061        1.38571
## Rattus_norvegicus_chr10.trna12848-LysCTT:tRNA 3847.5061        1.38571
## Rattus_norvegicus_chr10.trna12849-LysCTT:tRNA 3847.5061        1.38571
## Rattus_norvegicus_chr10.trna453-LysCTT:tRNA   3847.5061        1.38571
##                                                   lfcSE      stat      pvalue
##                                               <numeric> <numeric>   <numeric>
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA   0.345438   5.16406 2.41646e-07
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA  0.345438   5.16406 2.41646e-07
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA   0.345438   5.16406 2.41646e-07
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA    0.273486   4.65325 3.26747e-06
## Rattus_norvegicus_chrUn.trna406-LysCTT:tRNA    0.332283   4.57519 4.75787e-06
## Rattus_norvegicus_chr10.trna12028-LysCTT:tRNA  0.304203   4.55520 5.23355e-06
## Rattus_norvegicus_chr10.trna12844-LysCTT:tRNA  0.304203   4.55520 5.23355e-06
## Rattus_norvegicus_chr10.trna12848-LysCTT:tRNA  0.304203   4.55520 5.23355e-06
## Rattus_norvegicus_chr10.trna12849-LysCTT:tRNA  0.304203   4.55520 5.23355e-06
## Rattus_norvegicus_chr10.trna453-LysCTT:tRNA    0.304203   4.55520 5.23355e-06
##                                                      padj
##                                                 <numeric>
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA  2.87559e-05
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 2.87559e-05
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA  2.87559e-05
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA   1.43721e-04
## Rattus_norvegicus_chrUn.trna406-LysCTT:tRNA   1.43721e-04
## Rattus_norvegicus_chr10.trna12028-LysCTT:tRNA 1.43721e-04
## Rattus_norvegicus_chr10.trna12844-LysCTT:tRNA 1.43721e-04
## Rattus_norvegicus_chr10.trna12848-LysCTT:tRNA 1.43721e-04
## Rattus_norvegicus_chr10.trna12849-LysCTT:tRNA 1.43721e-04
## Rattus_norvegicus_chr10.trna453-LysCTT:tRNA   1.43721e-04
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## Wald test p-value: dosage 75 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                baseMean log2FoldChange
##                                               <numeric>      <numeric>
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA     222.461        2.42141
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA    162.416        3.02207
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA   162.416        3.02207
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA    162.416        3.02207
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA    563.986        2.38545
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA  31341.802       -1.22927
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA  30684.743       -1.37082
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA    28743.904       -1.47148
## Rattus_norvegicus_chr1.trna10113-ArgTCT:tRNA   8376.890       -1.30047
## Rattus_norvegicus_chr17.trna1626-SerGCT:tRNA    894.494       -1.69821
##                                                   lfcSE      stat      pvalue
##                                               <numeric> <numeric>   <numeric>
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA    0.272888   8.87327 7.10318e-19
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA   0.344733   8.76642 1.84442e-18
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA  0.344733   8.76642 1.84442e-18
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA   0.344733   8.76642 1.84442e-18
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA   0.282356   8.44836 2.95430e-17
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA   0.171136  -7.18298 6.82081e-13
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA   0.197738  -6.93250 4.13463e-12
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA     0.212689  -6.91846 4.56582e-12
## Rattus_norvegicus_chr1.trna10113-ArgTCT:tRNA   0.191409  -6.79418 1.08930e-11
## Rattus_norvegicus_chr17.trna1626-SerGCT:tRNA   0.250067  -6.79103 1.11337e-11
##                                                      padj
##                                                 <numeric>
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA   1.68303e-16
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA  1.68303e-16
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 1.68303e-16
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA  1.68303e-16
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA  2.15664e-15
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA  4.14932e-11
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA  2.08316e-10
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA    2.08316e-10
## Rattus_norvegicus_chr1.trna10113-ArgTCT:tRNA  4.06380e-10
## Rattus_norvegicus_chr17.trna1626-SerGCT:tRNA  4.06380e-10

Volcano plots for DESeq with Wald test

DESeq with likelihood ratio test

Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.

  • dosage 50mg vs 0mg results (only print the top 10 tRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                baseMean log2FoldChange
##                                               <numeric>      <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA    563.986       0.202367
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA     222.461       0.595371
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA    162.416       0.643676
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA   162.416       0.643676
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA    162.416       0.643676
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA  31341.802      -0.122000
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA     332.893       0.179741
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA    28743.904      -0.134518
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA  30684.743      -0.142406
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA    130.162       0.115244
##                                                   lfcSE      stat      pvalue
##                                               <numeric> <numeric>   <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA   0.276488   98.2044 3.78047e-21
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA    0.268494   92.2999 7.02262e-20
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA   0.340182   92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA  0.340182   92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA   0.340182   92.2545 7.18230e-20
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA   0.166770   61.2323 3.20581e-13
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA    0.286198   59.5201 7.44342e-13
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA     0.207268   56.4357 3.39125e-12
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA   0.192698   55.4838 5.41374e-12
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA   0.183660   54.9658 6.98262e-12
##                                                      padj
##                                                 <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA  1.37987e-18
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA   5.24308e-18
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA  5.24308e-18
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA  5.24308e-18
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA  1.95020e-11
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA   3.88121e-11
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA    1.54726e-10
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA  2.19557e-10
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA  2.54865e-10
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                baseMean log2FoldChange
##                                               <numeric>      <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA    563.986       1.045759
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA     222.461       1.272599
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA    162.416       1.783861
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA   162.416       1.783861
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA    162.416       1.783861
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA  31341.802      -0.645384
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA     332.893       0.937098
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA    28743.904      -0.777247
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA  30684.743      -0.687344
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA    130.162       0.356484
##                                                   lfcSE      stat      pvalue
##                                               <numeric> <numeric>   <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA   0.282667   98.2044 3.78047e-21
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA    0.273486   92.2999 7.02262e-20
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA   0.345438   92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA  0.345438   92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA   0.345438   92.2545 7.18230e-20
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA   0.171105   61.2323 3.20581e-13
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA    0.292310   59.5201 7.44342e-13
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA     0.212656   56.4357 3.39125e-12
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA   0.197707   55.4838 5.41374e-12
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA   0.186267   54.9658 6.98262e-12
##                                                      padj
##                                                 <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA  1.37987e-18
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA   5.24308e-18
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA  5.24308e-18
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA  5.24308e-18
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA  1.95020e-11
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA   3.88121e-11
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA    1.54726e-10
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA  2.19557e-10
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA  2.54865e-10
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                baseMean log2FoldChange
##                                               <numeric>      <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA    563.986        2.38545
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA     222.461        2.42141
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA    162.416        3.02207
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA   162.416        3.02207
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA    162.416        3.02207
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA  31341.802       -1.22927
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA     332.893        1.94155
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA    28743.904       -1.47148
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA  30684.743       -1.37082
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA    130.162        1.18445
##                                                   lfcSE      stat      pvalue
##                                               <numeric> <numeric>   <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA   0.282356   98.2044 3.78047e-21
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA    0.272888   92.2999 7.02262e-20
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA   0.344733   92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA  0.344733   92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA   0.344733   92.2545 7.18230e-20
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA   0.171136   61.2323 3.20581e-13
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA    0.292030   59.5201 7.44342e-13
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA     0.212689   56.4357 3.39125e-12
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA   0.197738   55.4838 5.41374e-12
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA   0.185481   54.9658 6.98262e-12
##                                                      padj
##                                                 <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA  1.37987e-18
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA   5.24308e-18
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA  5.24308e-18
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA  5.24308e-18
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA  1.95020e-11
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA   3.88121e-11
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA    1.54726e-10
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA  2.19557e-10
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA  2.54865e-10

Volcano plots for DESeq with likelihood ratio test

heatmap of counts

  • columns clustered
  • show tRNAs of top 20 mean counts



cDNA counts parsed from sRNAbench results

Repeat the above analysis on cDNA counts parsed from sRNAbench results

sample-wise heatmap

  • rows and columns clustered
  • label = library+dosages

PCA plots

  • From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder
  • The spectrum-like distribution of data over dosage PC1 still observable.
  • PC2 changed after removing Library_33

DESeq with Wald test

Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”

  • dosage 50mg vs 0mg results (only print the top 10 cDNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## Wald test p-value: dosage 50 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                           baseMean
##                                                          <numeric>
## ENSRNOT00000081838.1-ENSRNOG00000055604.1:protein_coding  30.54737
## ENSRNOT00000076099.1-ENSRNOG00000023577.7:protein_coding  29.10525
## ENSRNOT00000039592.5-ENSRNOG00000022181.5:protein_coding 111.20352
## ENSRNOT00000088851.1-ENSRNOG00000055769.1:protein_coding  27.14033
## ENSRNOT00000036094.2-ENSRNOG00000025987.2:protein_coding  42.32995
## ENSRNOT00000074649.2-ENSRNOG00000048205.2:protein_coding  31.64061
## ENSRNOT00000003770.6-ENSRNOG00000002810.6:protein_coding   9.85878
## ENSRNOT00000078734.1-ENSRNOG00000059091.1:protein_coding  93.65825
## ENSRNOT00000078034.1-ENSRNOG00000023541.6:protein_coding  10.10897
## ENSRNOT00000089975.1-ENSRNOG00000011180.3:protein_coding  13.34310
##                                                          log2FoldChange
##                                                               <numeric>
## ENSRNOT00000081838.1-ENSRNOG00000055604.1:protein_coding        4.11684
## ENSRNOT00000076099.1-ENSRNOG00000023577.7:protein_coding        3.59074
## ENSRNOT00000039592.5-ENSRNOG00000022181.5:protein_coding        2.85138
## ENSRNOT00000088851.1-ENSRNOG00000055769.1:protein_coding        4.05198
## ENSRNOT00000036094.2-ENSRNOG00000025987.2:protein_coding        3.72410
## ENSRNOT00000074649.2-ENSRNOG00000048205.2:protein_coding       -2.90100
## ENSRNOT00000003770.6-ENSRNOG00000002810.6:protein_coding        4.68979
## ENSRNOT00000078734.1-ENSRNOG00000059091.1:protein_coding        2.89674
## ENSRNOT00000078034.1-ENSRNOG00000023541.6:protein_coding        4.89123
## ENSRNOT00000089975.1-ENSRNOG00000011180.3:protein_coding        3.31740
##                                                              lfcSE      stat
##                                                          <numeric> <numeric>
## ENSRNOT00000081838.1-ENSRNOG00000055604.1:protein_coding  0.811775   5.07140
## ENSRNOT00000076099.1-ENSRNOG00000023577.7:protein_coding  0.763832   4.70096
## ENSRNOT00000039592.5-ENSRNOG00000022181.5:protein_coding  0.610595   4.66984
## ENSRNOT00000088851.1-ENSRNOG00000055769.1:protein_coding  0.875880   4.62618
## ENSRNOT00000036094.2-ENSRNOG00000025987.2:protein_coding  0.808794   4.60451
## ENSRNOT00000074649.2-ENSRNOG00000048205.2:protein_coding  0.636291  -4.55923
## ENSRNOT00000003770.6-ENSRNOG00000002810.6:protein_coding  1.031961   4.54454
## ENSRNOT00000078734.1-ENSRNOG00000059091.1:protein_coding  0.646072   4.48362
## ENSRNOT00000078034.1-ENSRNOG00000023541.6:protein_coding  1.090957   4.48343
## ENSRNOT00000089975.1-ENSRNOG00000011180.3:protein_coding  0.746282   4.44523
##                                                               pvalue       padj
##                                                            <numeric>  <numeric>
## ENSRNOT00000081838.1-ENSRNOG00000055604.1:protein_coding 3.94892e-07 0.00067487
## ENSRNOT00000076099.1-ENSRNOG00000023577.7:protein_coding 2.58938e-06 0.00134412
## ENSRNOT00000039592.5-ENSRNOG00000022181.5:protein_coding 3.01437e-06 0.00134412
## ENSRNOT00000088851.1-ENSRNOG00000055769.1:protein_coding 3.72470e-06 0.00134412
## ENSRNOT00000036094.2-ENSRNOG00000025987.2:protein_coding 4.13430e-06 0.00134412
## ENSRNOT00000074649.2-ENSRNOG00000048205.2:protein_coding 5.13417e-06 0.00134412
## ENSRNOT00000003770.6-ENSRNOG00000002810.6:protein_coding 5.50545e-06 0.00134412
## ENSRNOT00000078734.1-ENSRNOG00000059091.1:protein_coding 7.33869e-06 0.00139476
## ENSRNOT00000078034.1-ENSRNOG00000023541.6:protein_coding 7.34515e-06 0.00139476
## ENSRNOT00000089975.1-ENSRNOG00000011180.3:protein_coding 8.77987e-06 0.00150048
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## Wald test p-value: dosage 60 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                            baseMean
##                                                           <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding    37.3804
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron 1438.2370
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding   455.4459
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding   855.8283
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding   145.0713
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding   144.9098
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding   741.5106
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding    15.3069
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding    15.3069
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding    38.9553
##                                                           log2FoldChange
##                                                                <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding         4.49570
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron        3.71994
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding         3.82316
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding         3.75779
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding         3.15079
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding         3.14907
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding         3.32531
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding         5.48889
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding         5.48889
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding         7.41695
##                                                               lfcSE      stat
##                                                           <numeric> <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding   0.718753   6.25486
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron  0.602770   6.17140
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding   0.623665   6.13016
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding   0.619567   6.06518
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding   0.524450   6.00780
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding   0.528723   5.95599
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding   0.569331   5.84074
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding   0.941392   5.83061
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding   0.941392   5.83061
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding   1.272492   5.82868
##                                                                pvalue
##                                                             <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding  3.97868e-10
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron 6.76862e-10
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding  8.77935e-10
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding  1.31804e-09
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding  1.88060e-09
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding  2.58505e-09
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding  5.19705e-09
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding  5.52260e-09
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding  5.52260e-09
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding  5.58673e-09
##                                                                  padj
##                                                             <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding  8.13260e-07
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron 8.13260e-07
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding  8.13260e-07
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding  9.15710e-07
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding  1.04524e-06
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding  1.19731e-06
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding  1.55255e-06
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding  1.55255e-06
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding  1.55255e-06
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding  1.55255e-06
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## Wald test p-value: dosage 75 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                           baseMean
##                                                          <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding  102.4644
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding   37.3804
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding  455.4459
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding   74.3853
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding  922.2496
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding   51.3463
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding   72.4295
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding   72.4939
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding  741.5106
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding  145.0713
##                                                          log2FoldChange
##                                                               <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding        4.41460
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding        6.08154
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding        5.29364
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding        4.38967
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding        4.54005
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding        5.34662
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding        4.35744
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding        4.35745
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding        4.61055
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding        4.22637
##                                                              lfcSE      stat
##                                                          <numeric> <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding  0.505351   8.73572
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding  0.716043   8.49327
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding  0.623416   8.49135
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding  0.525921   8.34663
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding  0.550600   8.24565
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding  0.654719   8.16627
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding  0.534170   8.15741
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding  0.534553   8.15158
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding  0.569189   8.10021
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding  0.523801   8.06866
##                                                               pvalue
##                                                            <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 2.42103e-18
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.00909e-17
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 2.04250e-17
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 7.02361e-17
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding 1.64269e-16
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 3.18060e-16
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding 3.42292e-16
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding 3.59213e-16
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 5.48627e-16
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 7.10733e-16
##                                                                 padj
##                                                            <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 8.45422e-15
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.37747e-14
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 2.37747e-14
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 6.13161e-14
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding 1.14726e-13
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 1.56796e-13
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding 1.56796e-13
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding 1.56796e-13
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 2.12867e-13
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 2.48188e-13

Volcano plots for DESeq with Wald test

DESeq with likelihood ratio test

Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.

  • dosage 50mg vs 0mg results (only print the top 10 cDNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                           baseMean
##                                                          <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding   37.3804
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding   15.3069
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding   15.3069
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding   51.3463
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding  102.4644
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding   15.1979
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding   23.2678
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding  196.3968
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding   74.3853
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding   18.7590
##                                                          log2FoldChange
##                                                               <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding       2.721560
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding       2.224758
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding       2.224758
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding       1.603777
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding       1.666852
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding       2.014323
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding       1.500488
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding       0.950206
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding       1.723242
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding       1.081688
##                                                              lfcSE      stat
##                                                          <numeric> <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding  0.720490   89.6573
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding  0.990685   79.6212
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding  0.990685   79.6212
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding  0.657661   79.1794
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding  0.499279   78.8335
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding  1.015714   77.0973
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding  1.082014   74.9906
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding  0.454727   73.1212
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding  0.521159   72.7958
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding  0.683709   72.3783
##                                                               pvalue
##                                                            <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.59521e-19
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.60306e-17
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 5.46045e-17
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 1.28680e-16
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 3.64019e-16
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 9.15627e-16
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 1.07504e-15
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 1.32092e-15
##                                                                 padj
##                                                            <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 1.04509e-15
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.39785e-14
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 4.39785e-14
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 8.63660e-14
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 2.09415e-13
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 4.60904e-13
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 4.81022e-13
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 4.83575e-13
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                           baseMean
##                                                          <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding   37.3804
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding   15.3069
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding   15.3069
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding   51.3463
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding  102.4644
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding   15.1979
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding   23.2678
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding  196.3968
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding   74.3853
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding   18.7590
##                                                          log2FoldChange
##                                                               <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding        4.49570
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding        5.48889
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding        5.48889
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding        3.81202
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding        2.90946
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding        5.48895
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding        5.55555
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding        2.23837
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding        2.99666
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding        3.09041
##                                                              lfcSE      stat
##                                                          <numeric> <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding  0.718753   89.6573
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding  0.941392   79.6212
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding  0.941392   79.6212
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding  0.656801   79.1794
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding  0.506776   78.8335
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding  0.958362   77.0973
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding  1.019093   74.9906
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding  0.463618   73.1212
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding  0.527605   72.7958
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding  0.664670   72.3783
##                                                               pvalue
##                                                            <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.59521e-19
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.60306e-17
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 5.46045e-17
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 1.28680e-16
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 3.64019e-16
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 9.15627e-16
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 1.07504e-15
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 1.32092e-15
##                                                                 padj
##                                                            <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 1.04509e-15
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.39785e-14
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 4.39785e-14
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 8.63660e-14
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 2.09415e-13
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 4.60904e-13
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 4.81022e-13
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 4.83575e-13
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                           baseMean
##                                                          <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding   37.3804
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding   15.3069
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding   15.3069
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding   51.3463
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding  102.4644
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding   15.1979
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding   23.2678
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding  196.3968
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding   74.3853
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding   18.7590
##                                                          log2FoldChange
##                                                               <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding        6.08154
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding        6.93784
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding        6.93784
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding        5.34662
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding        4.41460
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding        6.93280
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding        7.31645
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding        3.70414
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding        4.38967
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding        4.61692
##                                                              lfcSE      stat
##                                                          <numeric> <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding  0.716043   89.6573
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding  0.937294   79.6212
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding  0.937294   79.6212
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding  0.654719   79.1794
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding  0.505351   78.8335
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding  0.954323   77.0973
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding  1.015716   74.9906
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding  0.462812   73.1212
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding  0.525921   72.7958
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding  0.659390   72.3783
##                                                               pvalue
##                                                            <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.59521e-19
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.60306e-17
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 5.46045e-17
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 1.28680e-16
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 3.64019e-16
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 9.15627e-16
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 1.07504e-15
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 1.32092e-15
##                                                                 padj
##                                                            <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 1.04509e-15
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.39785e-14
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 4.39785e-14
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 8.63660e-14
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 2.09415e-13
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 4.60904e-13
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 4.81022e-13
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 4.83575e-13

Volcano plots for DESeq with likelihood ratio test

heatmap of counts

  • columns clustered
  • show cDNAs of top 20 mean counts



ncRNA counts parsed from sRNAbench results

Repeat the above analysis on ncRNA counts parsed from sRNAbench results

sample-wise heatmap

  • rows and columns clustered
  • label = library+dosages

PCA plots

  • From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder
  • The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18).
  • The spectrum-like distribution of data over dosage PC1 still observable.
  • Library_06 as an outlier?

DESeq with Wald test

Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”

  • dosage 50mg vs 0mg results (only print the top 10 ncRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## Wald test p-value: dosage 50 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                                 baseMean
##                                                                <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA               79.90376
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA               15.15926
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA              141.39453
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript 141.14528
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA                 50.65957
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA                  19.15829
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript   6.92964
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript   5.93831
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA             498.99303
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript   5.73317
##                                                                log2FoldChange
##                                                                     <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA                    2.438197
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA                    3.435974
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA                    2.029514
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript       1.933846
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA                      2.115309
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA                       1.528495
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript       2.816321
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript       2.961914
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA                  -0.767382
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript       2.925478
##                                                                    lfcSE
##                                                                <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA               0.531396
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA               0.932182
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA               0.551362
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript  0.556530
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA                 0.634109
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA                  0.486329
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript  0.950787
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript  1.012509
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA              0.262394
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript  1.006380
##                                                                     stat
##                                                                <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA                4.58829
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA                3.68595
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA                3.68091
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript   3.47483
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA                  3.33588
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA                   3.14293
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript   2.96209
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript   2.92532
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA              -2.92454
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript   2.90693
##                                                                     pvalue
##                                                                  <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA              4.46893e-06
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA              2.27853e-04
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA              2.32400e-04
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript 5.11177e-04
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA                8.50309e-04
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA                 1.67268e-03
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript 3.05556e-03
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript 3.44101e-03
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA             3.44969e-03
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript 3.64994e-03
##                                                                       padj
##                                                                  <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA              0.000835689
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA              0.014486291
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA              0.014486291
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript 0.023897539
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA                0.031801553
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA                 0.046547166
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript 0.046547166
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript 0.046547166
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA             0.046547166
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript 0.046547166
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## Wald test p-value: dosage 60 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                    baseMean log2FoldChange
##                                                   <numeric>      <numeric>
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA      47.7074        1.73779
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA     50.6596        3.96580
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA   79.9038        3.00847
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA      19.1583        2.60094
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA  141.3945        3.02318
## ENSRNOT00000054649.3-ENSRNOG00000060018.1:rRNA      30.8831        1.90700
## ENSRNOT00000053226.3-ENSRNOG00000035103.3:rRNA      31.9729        1.77611
## ENSRNOT00000052795.3-ENSRNOG00000055521.1:rRNA      29.0141        1.91189
## ENSRNOT00000052439.3-ENSRNOG00000034316.3:rRNA      27.1848        1.95070
## ENSRNOT00000069467.1-ENSRNOG00000044200.1:rRNA      27.1848        1.95070
##                                                       lfcSE      stat
##                                                   <numeric> <numeric>
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA     0.274055   6.34103
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA    0.637457   6.22127
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA  0.541196   5.55894
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA     0.482084   5.39520
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA  0.562714   5.37250
## ENSRNOT00000054649.3-ENSRNOG00000060018.1:rRNA     0.359619   5.30283
## ENSRNOT00000053226.3-ENSRNOG00000035103.3:rRNA     0.358567   4.95337
## ENSRNOT00000052795.3-ENSRNOG00000055521.1:rRNA     0.398831   4.79373
## ENSRNOT00000052439.3-ENSRNOG00000034316.3:rRNA     0.407980   4.78135
## ENSRNOT00000069467.1-ENSRNOG00000044200.1:rRNA     0.407980   4.78135
##                                                        pvalue        padj
##                                                     <numeric>   <numeric>
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA    2.28241e-10 7.23525e-08
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA   4.93141e-10 7.81628e-08
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 2.71420e-08 2.86801e-06
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA    6.84457e-08 4.92323e-06
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 7.76535e-08 4.92323e-06
## ENSRNOT00000054649.3-ENSRNOG00000060018.1:rRNA    1.14019e-07 6.02398e-06
## ENSRNOT00000053226.3-ENSRNOG00000035103.3:rRNA    7.29399e-07 3.30314e-05
## ENSRNOT00000052795.3-ENSRNOG00000055521.1:rRNA    1.63713e-06 4.84662e-05
## ENSRNOT00000052439.3-ENSRNOG00000034316.3:rRNA    1.74121e-06 4.84662e-05
## ENSRNOT00000069467.1-ENSRNOG00000044200.1:rRNA    1.74121e-06 4.84662e-05
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## Wald test p-value: dosage 75 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                    baseMean log2FoldChange
##                                                   <numeric>      <numeric>
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA     50.6596        4.82891
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA      47.7074        2.03087
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA      49.8233        2.66563
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA      49.8233        2.66563
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA      49.8233        2.66563
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA      49.8233        2.66563
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA      49.8233        2.66563
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA      49.8233        2.66563
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA      49.8233        2.66563
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA  141.3945        4.00972
##                                                       lfcSE      stat
##                                                   <numeric> <numeric>
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA    0.636639   7.58500
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA     0.273975   7.41263
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA     0.359821   7.40820
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA     0.359821   7.40820
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA     0.359821   7.40820
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA     0.359821   7.40820
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA     0.359821   7.40820
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA     0.359821   7.40820
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA     0.359821   7.40820
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA  0.562269   7.13132
##                                                        pvalue        padj
##                                                     <numeric>   <numeric>
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA   3.32487e-14 5.07819e-12
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA    1.23816e-13 5.07819e-12
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA    1.28022e-13 5.07819e-12
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA    1.28022e-13 5.07819e-12
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA    1.28022e-13 5.07819e-12
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA    1.28022e-13 5.07819e-12
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA    1.28022e-13 5.07819e-12
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA    1.28022e-13 5.07819e-12
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA    1.28022e-13 5.07819e-12
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 9.94127e-13 3.54904e-11

Volcano plots for DESeq with Wald test

DESeq with likelihood ratio test

Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.

  • dosage 50mg vs 0mg results (only print the top 10 ncRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                      baseMean log2FoldChange
##                                                     <numeric>      <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA        49.8233       0.330634
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA        49.8233       0.330634
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA        49.8233       0.330634
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA        49.8233       0.330634
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA        49.8233       0.330634
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA        49.8233       0.330634
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA        49.8233       0.330634
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA        47.7074       0.675156
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense   11.7191       1.875690
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA       50.6596       2.115309
##                                                         lfcSE      stat
##                                                     <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA       0.365010   78.8606
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA       0.365010   78.8606
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA       0.365010   78.8606
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA       0.365010   78.8606
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA       0.365010   78.8606
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA       0.365010   78.8606
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA       0.365010   78.8606
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA       0.278194   75.5022
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense  0.940277   63.5641
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA      0.634109   63.1738
##                                                          pvalue        padj
##                                                       <numeric>   <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA      2.82794e-16 1.26197e-14
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 1.01733e-13 4.03541e-12
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA     1.23283e-13 4.40120e-12
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                      baseMean log2FoldChange
##                                                     <numeric>      <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA        49.8233        1.58630
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA        49.8233        1.58630
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA        49.8233        1.58630
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA        49.8233        1.58630
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA        49.8233        1.58630
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA        49.8233        1.58630
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA        49.8233        1.58630
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA        47.7074        1.73779
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense   11.7191        3.68295
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA       50.6596        3.96580
##                                                         lfcSE      stat
##                                                     <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA       0.361938   78.8606
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA       0.361938   78.8606
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA       0.361938   78.8606
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA       0.361938   78.8606
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA       0.361938   78.8606
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA       0.361938   78.8606
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA       0.361938   78.8606
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA       0.274055   75.5022
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense  0.911490   63.5641
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA      0.637457   63.1738
##                                                          pvalue        padj
##                                                       <numeric>   <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA      2.82794e-16 1.26197e-14
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 1.01733e-13 4.03541e-12
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA     1.23283e-13 4.40120e-12
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                      baseMean log2FoldChange
##                                                     <numeric>      <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA        49.8233        2.66563
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA        49.8233        2.66563
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA        49.8233        2.66563
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA        49.8233        2.66563
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA        49.8233        2.66563
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA        49.8233        2.66563
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA        49.8233        2.66563
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA        47.7074        2.03087
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense   11.7191        5.75993
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA       50.6596        4.82891
##                                                         lfcSE      stat
##                                                     <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA       0.359821   78.8606
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA       0.359821   78.8606
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA       0.359821   78.8606
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA       0.359821   78.8606
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA       0.359821   78.8606
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA       0.359821   78.8606
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA       0.359821   78.8606
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA       0.273975   75.5022
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense  0.903260   63.5641
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA      0.636639   63.1738
##                                                          pvalue        padj
##                                                       <numeric>   <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA      5.38795e-17 2.74785e-15
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA      2.82794e-16 1.26197e-14
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 1.01733e-13 4.03541e-12
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA     1.23283e-13 4.40120e-12

Volcano plots for DESeq with likelihood ratio test

heatmap of counts

  • columns clustered
  • show ncRNAs of top 20 mean counts



all RNA counts by another dataset parsed from sRNAbench results

Repeat the above analysis on a collection of different sRNA counts generated using another dataset. piRNA counts can be further extracted from the dataset.

sample-wise heatmap

  • rows and columns clustered
  • label = library+dosages

PCA plots

  • From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder
  • The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18).
  • The spectrum-like distribution of data over dosage PC1 still observable.
  • very much like the plot for cDNA, but PC2 did not change

DESeq with Wald test

Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”

  • dosage 50mg vs 0mg results (only print the top 10 RNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## Wald test p-value: dosage 50 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                 baseMean log2FoldChange
##                                                <numeric>      <numeric>
## URS0000CD0A72_10116:otherRNA:Rattus_norvegicus 5116.4435        3.99323
## URS0000CCF812_10116:otherRNA:Rattus_norvegicus 5116.1125        3.99296
## URS0000CD098B_10116:otherRNA:Rattus_norvegicus 5114.4670        3.99261
## URS0000CCE881_10116:otherRNA:Rattus_norvegicus 5114.6810        3.99254
## URS0000CD0070_10116:otherRNA:Rattus_norvegicus 5114.6810        3.99254
## URS0000CD00F9_10116:otherRNA:Rattus_norvegicus 5114.7556        3.99254
## URS0000CCE385_10116:otherRNA:Rattus_norvegicus 5114.4789        3.99246
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus  410.1260        3.22978
## URS00008C644C_10116:rRNA:Rattus_norvegicus      982.7875        3.37886
## URS0000B2DCD9_10116:lncRNA:Rattus_norvegicus     78.5454        3.28524
##                                                    lfcSE      stat      pvalue
##                                                <numeric> <numeric>   <numeric>
## URS0000CD0A72_10116:otherRNA:Rattus_norvegicus  0.733740   5.44229 5.25989e-08
## URS0000CCF812_10116:otherRNA:Rattus_norvegicus  0.733700   5.44223 5.26190e-08
## URS0000CD098B_10116:otherRNA:Rattus_norvegicus  0.733716   5.44163 5.27949e-08
## URS0000CCE881_10116:otherRNA:Rattus_norvegicus  0.733708   5.44160 5.28053e-08
## URS0000CD0070_10116:otherRNA:Rattus_norvegicus  0.733708   5.44160 5.28053e-08
## URS0000CD00F9_10116:otherRNA:Rattus_norvegicus  0.733711   5.44157 5.28123e-08
## URS0000CCE385_10116:otherRNA:Rattus_norvegicus  0.733709   5.44148 5.28403e-08
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus  0.599123   5.39085 7.01248e-08
## URS00008C644C_10116:rRNA:Rattus_norvegicus      0.651974   5.18251 2.18918e-07
## URS0000B2DCD9_10116:lncRNA:Rattus_norvegicus    0.649312   5.05957 4.20202e-07
##                                                       padj
##                                                  <numeric>
## URS0000CD0A72_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CCF812_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CD098B_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CCE881_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CD0070_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CD00F9_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CCE385_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus 0.000271374
## URS00008C644C_10116:rRNA:Rattus_norvegicus     0.000753052
## URS0000B2DCD9_10116:lncRNA:Rattus_norvegicus   0.001300904
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## Wald test p-value: dosage 60 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                              baseMean
##                                                             <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                    982.787
## URS0000246A92_10116:rRNA:Rattus_norvegicus                   2798.043
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus   326.394
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus                410.126
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus                    168.362
## URS000096C621_10116:rRNA:Rattus_norvegicus                    168.865
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                   5840.075
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                   3193.543
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus                137.043
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus                  133.566
##                                                             log2FoldChange
##                                                                  <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                         5.86837
## URS0000246A92_10116:rRNA:Rattus_norvegicus                         4.58837
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus        5.04313
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus                     4.64671
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus                         5.55086
## URS000096C621_10116:rRNA:Rattus_norvegicus                         5.67705
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                         3.88296
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                         3.93961
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus                     4.96512
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus                       5.62866
##                                                                 lfcSE      stat
##                                                             <numeric> <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                   0.667460   8.79208
## URS0000246A92_10116:rRNA:Rattus_norvegicus                   0.567077   8.09127
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus  0.652237   7.73205
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus               0.613641   7.57236
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus                   0.742889   7.47200
## URS000096C621_10116:rRNA:Rattus_norvegicus                   0.762465   7.44566
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                   0.521642   7.44373
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                   0.530930   7.42021
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus               0.674311   7.36325
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus                 0.769077   7.31873
##                                                                  pvalue
##                                                               <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                  1.46811e-18
## URS0000246A92_10116:rRNA:Rattus_norvegicus                  5.90465e-16
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 1.05832e-14
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus              3.66513e-14
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus                  7.89865e-14
## URS000096C621_10116:rRNA:Rattus_norvegicus                  9.64616e-14
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                  9.78813e-14
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                  1.16938e-13
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus              1.79489e-13
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus                2.50334e-13
##                                                                    padj
##                                                               <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                  1.46107e-14
## URS0000246A92_10116:rRNA:Rattus_norvegicus                  2.93815e-12
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 3.51080e-11
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus              9.11884e-11
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus                  1.39159e-10
## URS000096C621_10116:rRNA:Rattus_norvegicus                  1.39159e-10
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                  1.39159e-10
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                  1.45471e-10
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus              1.69252e-10
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus                1.69252e-10
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## Wald test p-value: dosage 75 vs 0 
## DataFrame with 10 rows and 6 columns
##                                                              baseMean
##                                                             <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                   982.7875
## URS0000246A92_10116:rRNA:Rattus_norvegicus                  2798.0432
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus  326.3940
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                  5840.0751
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus                97.3874
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                  3193.5427
## URS00008D1573_10116:rRNA:Rattus_norvegicus                  5439.5940
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus                  5527.3981
## URS00008C6232_10116:rRNA:Rattus_norvegicus                  6294.9675
## URS00008CA49B_10116:rRNA:Rattus_norvegicus                  6263.2736
##                                                             log2FoldChange
##                                                                  <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                         7.43903
## URS0000246A92_10116:rRNA:Rattus_norvegicus                         5.76099
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus        6.43684
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                         4.99015
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus                     6.99664
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                         4.99349
## URS00008D1573_10116:rRNA:Rattus_norvegicus                         4.98192
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus                         5.04692
## URS00008C6232_10116:rRNA:Rattus_norvegicus                         4.90935
## URS00008CA49B_10116:rRNA:Rattus_norvegicus                         4.88671
##                                                                 lfcSE      stat
##                                                             <numeric> <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                   0.667377  11.14667
## URS0000246A92_10116:rRNA:Rattus_norvegicus                   0.567059  10.15942
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus  0.652034   9.87194
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                   0.521634   9.56639
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus               0.740711   9.44585
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                   0.530917   9.40541
## URS00008D1573_10116:rRNA:Rattus_norvegicus                   0.530315   9.39428
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus                   0.538543   9.37143
## URS00008C6232_10116:rRNA:Rattus_norvegicus                   0.524199   9.36543
## URS00008CA49B_10116:rRNA:Rattus_norvegicus                   0.522451   9.35343
##                                                                  pvalue
##                                                               <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                  7.43361e-29
## URS0000246A92_10116:rRNA:Rattus_norvegicus                  3.00868e-24
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 5.50880e-23
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                  1.10704e-21
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus              3.52535e-21
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                  5.18277e-21
## URS00008D1573_10116:rRNA:Rattus_norvegicus                  5.76125e-21
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus                  7.15538e-21
## URS00008C6232_10116:rRNA:Rattus_norvegicus                  7.57407e-21
## URS00008CA49B_10116:rRNA:Rattus_norvegicus                  8.48487e-21
##                                                                    padj
##                                                               <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus                  9.62875e-25
## URS0000246A92_10116:rRNA:Rattus_norvegicus                  1.94857e-20
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 2.37851e-19
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus                  3.58486e-18
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus              9.13276e-18
## URS00008C6A58_10116:rRNA:Rattus_norvegicus                  9.63971e-18
## URS00008D1573_10116:rRNA:Rattus_norvegicus                  9.63971e-18
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus                  9.63971e-18
## URS00008C6232_10116:rRNA:Rattus_norvegicus                  9.63971e-18
## URS00008CA49B_10116:rRNA:Rattus_norvegicus                  9.63971e-18

Volcano plots for DESeq with Wald test

DESeq with likelihood ratio test

Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.

  • dosage 50mg vs 0mg results (only print the top 10 RNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                 baseMean log2FoldChange
##                                                <numeric>      <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus     5840.0751        1.28023
## URS00008C644C_10116:rRNA:Rattus_norvegicus      982.7875        3.37886
## URS0000246A92_10116:rRNA:Rattus_norvegicus     2798.0432        2.07124
## URS00008C6A58_10116:rRNA:Rattus_norvegicus     3193.5427        1.27246
## URS00008D1573_10116:rRNA:Rattus_norvegicus     5439.5940        1.24224
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus   97.3874        2.10002
## URS00008C6232_10116:rRNA:Rattus_norvegicus     6294.9675        1.22645
## URS00008CA49B_10116:rRNA:Rattus_norvegicus     6263.2736        1.22085
## URS00008CC58A_10116:rRNA:Rattus_norvegicus     6155.9577        1.22670
## URS00008CB810_10116:rRNA:Rattus_norvegicus     6345.8351        1.21114
##                                                    lfcSE      stat      pvalue
##                                                <numeric> <numeric>   <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus      0.508620   96.6120 8.31464e-21
## URS00008C644C_10116:rRNA:Rattus_norvegicus      0.651974   95.4563 1.47319e-20
## URS0000246A92_10116:rRNA:Rattus_norvegicus      0.553095   94.4255 2.45339e-20
## URS00008C6A58_10116:rRNA:Rattus_norvegicus      0.517829   93.8638 3.23945e-20
## URS00008D1573_10116:rRNA:Rattus_norvegicus      0.517095   93.8095 3.32772e-20
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus  0.740114   93.6848 3.53948e-20
## URS00008C6232_10116:rRNA:Rattus_norvegicus      0.511101   93.5596 3.76569e-20
## URS00008CA49B_10116:rRNA:Rattus_norvegicus      0.509397   93.4857 3.90602e-20
## URS00008CC58A_10116:rRNA:Rattus_norvegicus      0.512656   93.3636 4.14915e-20
## URS00008CB810_10116:rRNA:Rattus_norvegicus      0.511252   93.2325 4.42720e-20
##                                                      padj
##                                                 <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008C644C_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS0000246A92_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008C6A58_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008D1573_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 5.5086e-17
## URS00008C6232_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008CA49B_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008CC58A_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008CB810_10116:rRNA:Rattus_norvegicus     5.5086e-17
  • dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                 baseMean log2FoldChange
##                                                <numeric>      <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus     5840.0751        3.88296
## URS00008C644C_10116:rRNA:Rattus_norvegicus      982.7875        5.86837
## URS0000246A92_10116:rRNA:Rattus_norvegicus     2798.0432        4.58837
## URS00008C6A58_10116:rRNA:Rattus_norvegicus     3193.5427        3.93961
## URS00008D1573_10116:rRNA:Rattus_norvegicus     5439.5940        3.86076
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus   97.3874        5.38486
## URS00008C6232_10116:rRNA:Rattus_norvegicus     6294.9675        3.79468
## URS00008CA49B_10116:rRNA:Rattus_norvegicus     6263.2736        3.78503
## URS00008CC58A_10116:rRNA:Rattus_norvegicus     6155.9577        3.83198
## URS00008CB810_10116:rRNA:Rattus_norvegicus     6345.8351        3.80183
##                                                    lfcSE      stat      pvalue
##                                                <numeric> <numeric>   <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus      0.521642   96.6120 8.31464e-21
## URS00008C644C_10116:rRNA:Rattus_norvegicus      0.667460   95.4563 1.47319e-20
## URS0000246A92_10116:rRNA:Rattus_norvegicus      0.567077   94.4255 2.45339e-20
## URS00008C6A58_10116:rRNA:Rattus_norvegicus      0.530930   93.8638 3.23945e-20
## URS00008D1573_10116:rRNA:Rattus_norvegicus      0.530324   93.8095 3.32772e-20
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus  0.741492   93.6848 3.53948e-20
## URS00008C6232_10116:rRNA:Rattus_norvegicus      0.524207   93.5596 3.76569e-20
## URS00008CA49B_10116:rRNA:Rattus_norvegicus      0.522459   93.4857 3.90602e-20
## URS00008CC58A_10116:rRNA:Rattus_norvegicus      0.525797   93.3636 4.14915e-20
## URS00008CB810_10116:rRNA:Rattus_norvegicus      0.524363   93.2325 4.42720e-20
##                                                      padj
##                                                 <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008C644C_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS0000246A92_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008C6A58_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008D1573_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 5.5086e-17
## URS00008C6232_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008CA49B_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008CC58A_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008CB810_10116:rRNA:Rattus_norvegicus     5.5086e-17
  • dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0 
## LRT p-value: '~ dosage' vs '~ 1' 
## DataFrame with 10 rows and 6 columns
##                                                 baseMean log2FoldChange
##                                                <numeric>      <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus     5840.0751        4.99015
## URS00008C644C_10116:rRNA:Rattus_norvegicus      982.7875        7.43903
## URS0000246A92_10116:rRNA:Rattus_norvegicus     2798.0432        5.76099
## URS00008C6A58_10116:rRNA:Rattus_norvegicus     3193.5427        4.99349
## URS00008D1573_10116:rRNA:Rattus_norvegicus     5439.5940        4.98192
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus   97.3874        6.99664
## URS00008C6232_10116:rRNA:Rattus_norvegicus     6294.9675        4.90935
## URS00008CA49B_10116:rRNA:Rattus_norvegicus     6263.2736        4.88671
## URS00008CC58A_10116:rRNA:Rattus_norvegicus     6155.9577        4.91559
## URS00008CB810_10116:rRNA:Rattus_norvegicus     6345.8351        4.89185
##                                                    lfcSE      stat      pvalue
##                                                <numeric> <numeric>   <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus      0.521634   96.6120 8.31464e-21
## URS00008C644C_10116:rRNA:Rattus_norvegicus      0.667377   95.4563 1.47319e-20
## URS0000246A92_10116:rRNA:Rattus_norvegicus      0.567059   94.4255 2.45339e-20
## URS00008C6A58_10116:rRNA:Rattus_norvegicus      0.530917   93.8638 3.23945e-20
## URS00008D1573_10116:rRNA:Rattus_norvegicus      0.530315   93.8095 3.32772e-20
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus  0.740711   93.6848 3.53948e-20
## URS00008C6232_10116:rRNA:Rattus_norvegicus      0.524199   93.5596 3.76569e-20
## URS00008CA49B_10116:rRNA:Rattus_norvegicus      0.522451   93.4857 3.90602e-20
## URS00008CC58A_10116:rRNA:Rattus_norvegicus      0.525789   93.3636 4.14915e-20
## URS00008CB810_10116:rRNA:Rattus_norvegicus      0.524355   93.2325 4.42720e-20
##                                                      padj
##                                                 <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008C644C_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS0000246A92_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008C6A58_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008D1573_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 5.5086e-17
## URS00008C6232_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008CA49B_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008CC58A_10116:rRNA:Rattus_norvegicus     5.5086e-17
## URS00008CB810_10116:rRNA:Rattus_norvegicus     5.5086e-17

Volcano plots for DESeq with likelihood ratio test

heatmap of counts

  • columns clustered
  • show RNAs of top 20 mean counts